It is hoped a native fish species in the Murray's lower lakes can be saved by opening the Goolwa barrage near the river mouth in South Australia.

SA Environment Minister Paul Caica says congolli have not bred for three years because low water levels during drought times have separated male and female fish populations.

Mr Caica says opening the boating lock will give the fish a chance to meet and breed.

"The trial that we conducted last week we used the boat lock and we saw almost 800 congolli swim into the lock chamber after the upstream gate was opened," he said.

"We also saw other fish species that were able to swim up or downstream.

"It provides that connectivity for part of the congolli population in the region."

Environment Department ecologist Jason Higham said the females usually swam downstream past the barrage to breed, but the low water had interrupted that journey.

"The barrage still serves a very important function in terms of helping to maintain the lakes as a freshwater environment in normal conditions but it had the unintended consequences of creating a physical barrier which stopped the movement of species," he said.

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